INNER CODE UNIT · Python

run

MariaNattestad/assemblytics · assemblytics/dotplot.py:10

def run(output_dir):
    filename = os.path.join(output_dir, "assemblytics_oriented_coords.csv")
    plot_output_filename = os.path.join(output_dir, "assemblytics_dotplot_filtered")
    plot_title = "Dot plot of Assemblytics filtered alignments"

    if not os.path.exists(filename):
        print(f"File {filename} not found.")
        return

    coords = pd.read_csv(filename)

    if len(coords) > 100000:
        coords = coords.head(100000)

    coords['ref'] = coords['ref'].astype(str)
    coords['query'] = coords['query'].astype(str)

    # Ordering chromosomes

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